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Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX.

Nucleic Acids Res. 2012 Sep;40(16):7690-704.


Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.


Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T.

Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Review.


Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.


Genome-wide map of regulatory interactions in the human genome.

Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP.

Genome Res. 2014 Dec;24(12):1905-17. doi: 10.1101/gr.176586.114.


Transcriptional regulation and spatial interactions of head-to-head genes.

Chen Y, Li Y, Wei J, Li YY.

BMC Genomics. 2014 Jun 24;15:519. doi: 10.1186/1471-2164-15-519.


An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape.

Chen H, Li H, Liu F, Zheng X, Wang S, Bo X, Shu W.

Sci Rep. 2015 Feb 16;5:8465. doi: 10.1038/srep08465.


Sequence and chromatin determinants of cell-type-specific transcription factor binding.

Arvey A, Agius P, Noble WS, Leslie C.

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.


Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.

Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, Weiss MJ, Hardison RC.

Genome Res. 2014 Dec;24(12):1945-62. doi: 10.1101/gr.164830.113.


Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

He A, Kong SW, Ma Q, Pu WT.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5632-7. doi: 10.1073/pnas.1016959108.


Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.

Kumar S, Bucher P.

BMC Bioinformatics. 2016 Jan 11;17 Suppl 1:4. doi: 10.1186/s12859-015-0846-z.


Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana.

Wang J, Zhou Y, Li X, Meng X, Fan M, Chen H, Xue J, Chen M.

Plant Cell Physiol. 2016 Nov 15. pii: pcw194. doi: 10.1093/pcp/pcw194. [Epub ahead of print]


On the identification of potential regulatory variants within genome wide association candidate SNP sets.

Chen CY, Chang IS, Hsiung CA, Wasserman WW.

BMC Med Genomics. 2014 Jun 11;7:34. doi: 10.1186/1755-8794-7-34.


Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ.

Genome Res. 2013 Dec;23(12):2136-48. doi: 10.1101/gr.158261.113.


Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-Seq.

Hitchler MJ, Rice JC.

Methods Mol Biol. 2011;767:253-67. doi: 10.1007/978-1-61779-201-4_19.


MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets.

Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ.

Genome Biol. 2012 Mar 16;13(3):R16. doi: 10.1186/gb-2012-13-3-r16.


ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

Hon G, Ren B, Wang W.

PLoS Comput Biol. 2008 Oct;4(10):e1000201. doi: 10.1371/journal.pcbi.1000201.


The functional consequences of variation in transcription factor binding.

Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y.

PLoS Genet. 2014 Mar 6;10(3):e1004226. doi: 10.1371/journal.pgen.1004226.


Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy.

Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH.

Mol Cell. 2009 Nov 25;36(4):667-81. doi: 10.1016/j.molcel.2009.11.001.

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